1. Creation of an OpenTox dataset from a local file

Download the TCAMS subset from the link mentioned in the introduction to this tutorial
and save it to your computer. Open the file and take a look at it. The
OpenTox dataset service implemented in the Ambit2 application allows
many different file formats for uploading and creating OpenTox datasets
(SDF, MOL, SMI, CSV, TXT, ToxML (.xml)). In this tutorial, we will use a
CSV file. Note that in this tutorial we won't actually upload the data file
containing the 87 TCAMS compounds, to avoid repeated uploading of the
same dataset by every user of this tutorial. We will only take you
through the steps of how to do the upload, but we will leave the final
click of the "Upload" button aside.

To upload the data, navigate in your web browser to http://apps.ideaconsult.net:8080/ambit2/. Navigate to "Datasets" using the links given at the top of the page ("Datasets" is the third from the left).

The box at the top left is for adding a new dataset.
Browse for the file on your computer, and give a name to the dataset,
for example "TCAMS WorkshopMunich Dataset". Select "Match by SMILES"
from the dropdown list under "Match". This way, on import the
application will check if any of the compounds are already present in
the database, based on the SMILES used. IMPORTANT: Don't click "Submit" at the end. The dataset we are working with in this tutorial already exists, and there's no need to add another version of it.

Assuming you had uploaded the data file and had given it
the name "TCAMS WorkshopMunich Dataset", let's find the dataset in
Ambit2. For this, stay at, or go back to the datasets page of Ambit2 (http://apps.ideaconsult.net:8080/ambit2/dataset).
The available datasets are listed according to their names' first
letter. Thus, navigate to "T" to find the TCAMS WorkshopMunich Dataset.